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Kumari S, Bodhale N, Sarode A, Jha MK, Bhadange S, Pandey SP, Selvaraj S, Chande AG, Mukhopadhyaya R, Ghosh SK, Singh S, Mukherjee D, Duffin R, Andrews P, Saha B. Leishmania major MAPK4 intercepts and redirects CD40 signaling promoting infection. Int Immunopharmacol 2024; 134:112100. [PMID: 38728877 DOI: 10.1016/j.intimp.2024.112100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/06/2024] [Accepted: 04/13/2024] [Indexed: 05/12/2024]
Abstract
The parasite Leishmania resides as amastigotes within the macrophage parasitophorous vacuoles inflicting the disease Leishmaniasis. Leishmania selectively modulates mitogen-activated protein kinase (MAPK) phosphorylation subverting CD40-triggered anti-leishmanial functions of macrophages. The mechanism of any pathogen-derived molecule induced host MAPK modulation remains poorly understood. Herein, we show that of the fifteen MAPKs, LmjMAPK4 expression is higher in virulent L. major. LmjMAPK4- detected in parasitophorous vacuoles and cytoplasm- binds MEK-1/2, but not MKK-3/6. Lentivirally-overexpressed LmjMAPK4 augments CD40-activated MEK-1/2-ERK-1/2-MKP-1, but inhibits MKK3/6-p38MAPK-MKP-3, phosphorylation. A rationally-identified LmjMAPK4 inhibitor reinstates CD40-activated host-protective anti-leishmanial functions in L. major-infected susceptible BALB/c mice. These results identify LmjMAPK4 as a MAPK modulator at the host-pathogen interface and establish a pathogen-intercepted host receptor signaling as a scientific rationale for identifying drug targets.
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Affiliation(s)
- Sangeeta Kumari
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Neelam Bodhale
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Aditya Sarode
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Mukesh Kumar Jha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Sagar Bhadange
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | | | | | - Ajit G Chande
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | | | | | - Shailza Singh
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | | | - Rebekah Duffin
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Philip Andrews
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
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2
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Asencio C, Hervé P, Morand P, Oliveres Q, Morel CA, Prouzet-Mauleon V, Biran M, Monic S, Bonhivers M, Robinson DR, Ouellette M, Rivière L, Bringaud F, Tetaud E. Streptococcus pyogenes Cas9 ribonucleoprotein delivery for efficient, rapid and marker-free gene editing in Trypanosoma and Leishmania. Mol Microbiol 2024; 121:1079-1094. [PMID: 38558208 DOI: 10.1111/mmi.15256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Kinetoplastids are unicellular eukaryotic flagellated parasites found in a wide range of hosts within the animal and plant kingdoms. They are known to be responsible in humans for African sleeping sickness (Trypanosoma brucei), Chagas disease (Trypanosoma cruzi), and various forms of leishmaniasis (Leishmania spp.), as well as several animal diseases with important economic impact (African trypanosomes, including Trypanosoma congolense). Understanding the biology of these parasites necessarily implies the ability to manipulate their genomes. In this study, we demonstrate that transfection of a ribonucleoprotein complex, composed of recombinant Streptococcus pyogenes Cas9 (SpCas9) and an in vitro-synthesized guide RNA, results in rapid and efficient genetic modifications of trypanosomatids, in marker-free conditions. This approach was successfully developed to inactivate, delete, and mutate candidate genes in various stages of the life cycle of T. brucei and T. congolense, and Leishmania promastigotes. The functionality of SpCas9 in these parasites now provides, to the research community working on these parasites, a rapid and efficient method of genome editing, without requiring plasmid construction and selection by antibiotics but requires only cloning and PCR screening of the clones. Importantly, this approach is adaptable to any wild-type parasite.
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Affiliation(s)
| | - Perrine Hervé
- Univ. Bordeaux, CNRS, MFP, UMR 5234, Bordeaux, France
| | | | | | | | | | - Marc Biran
- Univ. Bordeaux, CNRS, CRMSB, UMR 5536, Bordeaux, France
| | - Sarah Monic
- Univ. Bordeaux, CNRS, MFP, UMR 5234, Bordeaux, France
| | | | | | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec, Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Loïc Rivière
- Univ. Bordeaux, CNRS, MFP, UMR 5234, Bordeaux, France
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3
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Trajano-Silva LAM, Mule SN, Palmisano G. Molecular tools to regulate gene expression in Trypanosoma cruzi. Adv Clin Chem 2024; 120:169-190. [PMID: 38762241 DOI: 10.1016/bs.acc.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Developing molecular strategies to manipulate gene expression in trypanosomatids is challenging, particularly with respect to the unique gene expression mechanisms adopted by these unicellular parasites, such as polycistronic mRNA transcription and multi-gene families. In the case of Trypanosoma cruzi (T. cruzi), the causative agent of Chagas Disease, the lack of RNA interference machinery further complicated functional genetic studies important for understanding parasitic biology and developing biomarkers and potential therapeutic targets. Therefore, alternative methods of performing knockout and/or endogenous labelling experiments were developed to identify and understand the function of proteins for survival and interaction with the host. In this review, we present the main tools for the genetic manipulation of T. cruzi, focusing on the Clustered Regularly Interspaced Short Palindromic Repeats Cas9-associated system technique widely used in this organism. Moreover, we highlight the importance of using these tools to elucidate the function of uncharacterized and glycosylated proteins. Further developments of these technologies will allow the identification of new biomarkers, therapeutic targets and potential vaccines against Chagas disease with greater efficiency and speed.
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Affiliation(s)
- Lays Adrianne M Trajano-Silva
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Simon Ngao Mule
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
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4
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Fesser A, Beilstein S, Kaiser M, Schmidt RS, Mäser P. Trypanosoma cruzi STIB980: A TcI Strain for Drug Discovery and Reverse Genetics. Pathogens 2023; 12:1217. [PMID: 37887733 PMCID: PMC10610277 DOI: 10.3390/pathogens12101217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
Since the first published genome sequence of Trypanosoma cruzi in 2005, there have been tremendous technological advances in genomics, reverse genetics, and assay development for this elusive pathogen. However, there is still an unmet need for new and better drugs to treat Chagas disease. Here, we introduce a T. cruzi assay strain that is useful for drug research and basic studies of host-pathogen interactions. T. cruzi STIB980 is a strain of discrete typing unit TcI that grows well in culture as axenic epimastigotes or intracellular amastigotes. We evaluated the optimal parameters for genetic transfection and constructed derivatives of T. cruzi STIB980 that express reporter genes for fluorescence- or bioluminescence-based drug efficacy testing, as well as a Cas9-expressing line for CRISPR/Cas9-mediated gene editing. The genome of T. cruzi STIB980 was sequenced by combining short-read Illumina with long-read Oxford Nanopore technologies. The latter served as the primary assembly and the former to correct mistakes. This resulted in a high-quality nuclear haplotype assembly of 28 Mb in 400 contigs, containing 10,043 open-reading frames with a median length of 1077 bp. We believe that T. cruzi STIB980 is a useful addition to the antichagasic toolbox and propose that it can serve as a DTU TcI reference strain for drug efficacy testing.
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Affiliation(s)
- Anna Fesser
- Swiss Tropical and Public Health Institute, Department Medical Parasitology and Infection Biology, 4123 Allschwil, Switzerland
- University of Basel, 4001 Basel, Switzerland
| | - Sabina Beilstein
- Swiss Tropical and Public Health Institute, Department Medical Parasitology and Infection Biology, 4123 Allschwil, Switzerland
- University of Basel, 4001 Basel, Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Department Medical Parasitology and Infection Biology, 4123 Allschwil, Switzerland
- University of Basel, 4001 Basel, Switzerland
| | - Remo S Schmidt
- Swiss Tropical and Public Health Institute, Department Medical Parasitology and Infection Biology, 4123 Allschwil, Switzerland
- University of Basel, 4001 Basel, Switzerland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Department Medical Parasitology and Infection Biology, 4123 Allschwil, Switzerland
- University of Basel, 4001 Basel, Switzerland
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5
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Gaona-López C, Martínez-Vázquez AV, Villalobos-Rocha JC, Juárez-Rendón KJ, Rivera G. Analysis of Giardia lamblia Nucleolus as Drug Target: A Review. Pharmaceuticals (Basel) 2023; 16:1168. [PMID: 37631082 PMCID: PMC10457859 DOI: 10.3390/ph16081168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Giardia lamblia (G. lamblia) is the main causative agent of diarrhea worldwide, affecting children and adults alike; in the former, it can be lethal, and in the latter a strong cause of morbidity. Despite being considered a predominant disease in low-income and developing countries, current migratory flows have caused an increase in giardiasis cases in high-income countries. Currently, there is a wide variety of chemotherapeutic treatments to combat this parasitosis, most of which have potentially serious side effects, such as genotoxic, carcinogenic, and teratogenic. The necessity to create novel treatments and discover new therapeutic targets to fight against this illness is evident. The current review centers around the controversial nucleolus of G. lamblia, providing a historical perspective that traces its apparent absence to the present evidence supporting its existence as a subnuclear compartment in this organism. Additionally, possible examples of ncRNAs and proteins ubiquitous to the nucleolus that can be used as targets of different therapeutic strategies are discussed. Finally, some examples of drugs under research that could be effective against G. lamblia are described.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | | | - Juan Carlos Villalobos-Rocha
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico;
| | - Karina Janett Juárez-Rendón
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico; (A.V.M.-V.); (K.J.J.-R.)
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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6
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Gaona-López C, Vazquez-Jimenez LK, Gonzalez-Gonzalez A, Delgado-Maldonado T, Ortiz-Pérez E, Nogueda-Torres B, Moreno-Rodríguez A, Vázquez K, Saavedra E, Rivera G. Advances in Protozoan Epigenetic Targets and Their Inhibitors for the Development of New Potential Drugs. Pharmaceuticals (Basel) 2023; 16:ph16040543. [PMID: 37111300 PMCID: PMC10143871 DOI: 10.3390/ph16040543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Protozoan parasite diseases cause significant mortality and morbidity worldwide. Factors such as climate change, extreme poverty, migration, and a lack of life opportunities lead to the propagation of diseases classified as tropical or non-endemic. Although there are several drugs to combat parasitic diseases, strains resistant to routinely used drugs have been reported. In addition, many first-line drugs have adverse effects ranging from mild to severe, including potential carcinogenic effects. Therefore, new lead compounds are needed to combat these parasites. Although little has been studied regarding the epigenetic mechanisms in lower eukaryotes, it is believed that epigenetics plays an essential role in vital aspects of the organism, from controlling the life cycle to the expression of genes involved in pathogenicity. Therefore, using epigenetic targets to combat these parasites is foreseen as an area with great potential for development. This review summarizes the main known epigenetic mechanisms and their potential as therapeutics for a group of medically important protozoal parasites. Different epigenetic mechanisms are discussed, highlighting those that can be used for drug repositioning, such as histone post-translational modifications (HPTMs). Exclusive parasite targets are also emphasized, including the base J and DNA 6 mA. These two categories have the greatest potential for developing drugs to treat or eradicate these diseases.
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Affiliation(s)
- Carlos Gaona-López
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Lenci K Vazquez-Jimenez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Alonzo Gonzalez-Gonzalez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Timoteo Delgado-Maldonado
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Eyrá Ortiz-Pérez
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
| | - Benjamín Nogueda-Torres
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Adriana Moreno-Rodríguez
- Laboratorio de Estudios Epidemiológicos, Clínicos, Diseños Experimentales e Investigación, Facultad de Ciencias Químicas, Universidad Autónoma "Benito Juárez" de Oaxaca, Avenida Universidad S/N, Ex Hacienda Cinco Señores, Oaxaca 68120, Mexico
| | - Karina Vázquez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Nuevo León, Francisco Villa 20, General Escobedo 66054, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnología Farmacéutica, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Mexico
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An RNA Interference (RNAi) Toolkit and Its Utility for Functional Genetic Analysis of Leishmania ( Viannia). Genes (Basel) 2022; 14:genes14010093. [PMID: 36672832 PMCID: PMC9858808 DOI: 10.3390/genes14010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool whose efficacy against a broad range of targets enables functional genetic tests individually or systematically. However, the RNAi pathway has been lost in evolution by a variety of eukaryotes including most Leishmania sp. RNAi was retained in species of the Leishmania subgenus Viannia, and here we describe the development, optimization, and application of RNAi tools to the study of L. (Viannia) braziliensis (Lbr). We developed vectors facilitating generation of long-hairpin or "stem-loop" (StL) RNAi knockdown constructs, using GatewayTM site-specific recombinase technology. A survey of applications of RNAi in L. braziliensis included genes interspersed within multigene tandem arrays such as quinonoid dihydropteridine reductase (QDPR), a potential target or modulator of antifolate sensitivity. Other tests include genes involved in cell differentiation and amastigote proliferation (A600), and essential genes of the intraflagellar transport (IFT) pathway. We tested a range of stem lengths targeting the L. braziliensis hypoxanthine-guanine phosphoribosyl transferase (HGPRT) and reporter firefly luciferase (LUC) genes and found that the efficacy of RNAi increased with stem length, and fell off greatly below about 128 nt. We used the StL length dependency to establish a useful 'hypomorphic' approach not possible with other gene ablation strategies, with shorter IFT140 stems yielding viable cells with compromised flagellar morphology. We showed that co-selection for RNAi against adenine phosphoryl transferase (APRT1) using 4-aminopyrazolpyrimidine (APP) could increase the efficacy of RNAi against reporter constructs, a finding that may facilitate improvements in future work. Thus, for many genes, RNAi provides a useful tool for studying Leishmania gene function with some unique advantages.
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8
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Pal S, Dam S. CRISPR-Cas9: Taming protozoan parasites with bacterial scissor. J Parasit Dis 2022; 46:1204-1212. [PMID: 36457766 PMCID: PMC9606157 DOI: 10.1007/s12639-022-01534-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022] Open
Abstract
The invention of CRISPR-Cas9 technology has opened a new era in which genome manipulation has become precise, faster, cheap and more accurate than previous genome editing strategies. Despite the intricacies of the genomes associated with several protozoan parasites, CRISPR-Cas9 has made a substantial contribution to parasitology. The study of functional genomics through CRISPR-Cas9 mediated gene knockout, insertion, deletion and mutation has helped in understanding intrinsic parasite biology. The invention of CRISPR-dCas9 has helped in the programmable control of protozoan gene expression and epigenetic engineering. CRISPR and CRISPR-based alternatives will continue to thrive and may aid in the development of novel anti-protozoan strategies to tame the protozoan parasites in the imminent future.
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Affiliation(s)
- Suchetana Pal
- Department of Microbiology, The University of Burdwan, Burdwan, West Bengal 713104 India
| | - Somasri Dam
- Department of Microbiology, The University of Burdwan, Burdwan, West Bengal 713104 India
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Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects. Nat Commun 2022; 13:5326. [PMID: 36088375 PMCID: PMC9464253 DOI: 10.1038/s41467-022-33109-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Trypanosomatids, which include major pathogens of humans and livestock, are flagellated protozoa for which cell cycle controls and the underlying mechanisms are not completely understood. Here, we describe a genome-wide RNA-interference library screen for cell cycle defects in Trypanosoma brucei. We induced massive parallel knockdown, sorted the perturbed population using high-throughput flow cytometry, deep-sequenced RNAi-targets from each stage and digitally reconstructed cell cycle profiles at a genomic scale; also enabling data visualisation using an online tool ( https://tryp-cycle.pages.dev/ ). Analysis of several hundred genes that impact cell cycle progression reveals >100 flagellar component knockdowns linked to genome endoreduplication, evidence for metabolic control of the G1-S transition, surface antigen regulatory mRNA-binding protein knockdowns linked to G2M accumulation, and a putative nucleoredoxin required for both mitochondrial genome segregation and for mitosis. The outputs provide comprehensive functional genomic evidence for the known and novel machineries, pathways and regulators that coordinate trypanosome cell cycle progression.
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Zhang L, Chen L, Zhang H, Si H, Liu X, Suo X, Hu D. A comparative study of microRNAs in different stages of Eimeria tenella. Front Vet Sci 2022; 9:954725. [PMID: 35937295 PMCID: PMC9353057 DOI: 10.3389/fvets.2022.954725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Apicomplexan parasites have divergent biogenesis machinery for small RNA generation. Analysis has shown that parasites in Plasmodium and Cryptosporidium as well as many species in Leishmania or Trypanosoma do not have a complete machinery in small RNA biogenesis. Recently, the miRNA-generating system of Toxoplasma has been identified as plant/fungal-like and its miRNAome has been elucidated. However, the microRNA (miRNA) expression profiles and their potential regulatory functions in different stages of Eimeria tenella remain largely unknown. In this study, we characterized the RNA silencing machinery of E. tenella and investigated the miRNA population distribution at different life stages by high-throughput sequencing. We characterized the expression of miRNAs in the unsporulated oocyst, sporulated oocyst and schizogony stages, obtaining a total of 392 miRNAs. We identified 58 differentially expressed miRNAs between USO (unsporulated oocysts) and SO (sporulated oocysts) that were significantly enriched for their potential target genes in the regulation of gene expression and chromatin binding, suggesting an epigenetic modulation of sporulating by these miRNAs. In comparing miRNA expression at endogenous and exogenous developmental stages, twenty-four miRNAs were identified differently expressed. Those were mainly associated with the regulation of genes with protein kinase activity, suggesting control of protein phosphorylation. This is the first study about the evolution of miRNA biogenesis system and miRNA control of gene expression in Eimeria species. Our data may lead to functional insights into of the regulation of gene expression during parasite life cycle in apicomplexan parasites.
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Affiliation(s)
- Lei Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Linlin Chen
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hongtao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hongbin Si
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xianyong Liu
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xun Suo
- Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Dandan Hu
- College of Animal Science and Technology, Guangxi University, Nanning, China
- *Correspondence: Dandan Hu
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11
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Zhou Z, Eichner C, Nilsen F, Jonassen I, Dondrup M. A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis). BMC Genomics 2021; 22:832. [PMID: 34789144 PMCID: PMC8600823 DOI: 10.1186/s12864-021-08054-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/04/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. METHODS Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. RESULTS Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. CONCLUSIONS We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.
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Affiliation(s)
- Zhaoran Zhou
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Christiane Eichner
- Department of Biological Sciences & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Frank Nilsen
- Department of Biological Sciences & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Inge Jonassen
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
| | - Michael Dondrup
- Department of Informatics & Sea Lice Research Centre, University of Bergen, Thormøhlensgate 55, Bergen, 5008 Norway
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12
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RISC in Entamoeba histolytica: Identification of a Protein-Protein Interaction Network for the RNA Interference Pathway in a Deep-Branching Eukaryote. mBio 2021; 12:e0154021. [PMID: 34488447 PMCID: PMC8546589 DOI: 10.1128/mbio.01540-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Entamoeba histolytica is a protozoan parasite that causes amebiasis in humans and is a major health concern in developing countries. Our previous work revealed a functional RNA interference (RNAi) pathway in Entamoeba. Several unusual features encompass the RNAi pathway in the parasite, including small RNAs (sRNAs) with a 5'-polyphosphate structure (identified to date only in Entamoeba and nematodes) and the conspicuous absence of a canonical Dicer enzyme. Currently, little is known about the Entamoeba RNA-induced silencing complex (RISC), which is critical in understanding how RNAi is achieved in the parasite. In this study, we examined the RISC of EhAgo2-2, the most highly expressed Argonaute protein in Entamoeba. We identified 43 protein components of EhAgo2-2 RISC with a broad range of functional activities. Two proteins with nucleosome assembly protein (NAP) domains, not previously observed in other RNAi systems, were identified as novel core members of amebic RISC. We further demonstrated the interaction of these NAPs with Ago using an in vitro recombinant system. Finally, we characterized the interaction network of five RISC components identified in this study to further elucidate the interactions of these RNAi pathway proteins. Our data suggest the presence of closely interacting protein groups within RISC and allowed us to build a map of protein-protein interactions in relation to Ago. Our work is the first to elucidate RISC components in Entamoeba and expands the current knowledge of RISC to a deep-branching single-celled eukaryote. IMPORTANCE Entamoeba histolytica is a leading parasitic cause of death in developing countries, and our efforts are focused on defining the molecular basis of RNA interference (RNAi) gene regulation in this parasite. The Entamoeba RNAi pathway effectively silences a subset of endogenous genes and has also been harnessed as a gene silencing tool to study gene function in this organism. However, little is known about the components of the Entamoeba RNA-induced silencing complex (RISC), which is critical in understanding how gene silencing is achieved in the parasite. This study characterizes, for the first time, the RISC components in Entamoeba and provides new insights in understanding the molecular regulatory mechanisms of RNAi in this parasite, including the demonstration of novel Ago protein-interacting partners. From an evolutionary point of view, our findings expand the current knowledge of RISC to a deep-branching single-celled eukaryote.
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Kaur P, Goyal N. Pathogenic role of mitogen activated protein kinases in protozoan parasites. Biochimie 2021; 193:78-89. [PMID: 34706251 DOI: 10.1016/j.biochi.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/29/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
Protozoan parasites with complex life cycles have high mortality rates affecting billions of human lives. Available anti-parasitic drugs are inadequate due to variable efficacy, toxicity, poor patient compliance and drug-resistance. Hence, there is an urgent need for the development of safer and better chemotherapeutics. Mitogen Activated Protein Kinases (MAPKs) have drawn much attention as potential drug targets. This review summarizes unique structural and functional features of MAP kinases and their possible role in pathogenesis of obligate intracellular protozoan parasites namely, Leishmania, Trypanosoma, Plasmodium and Toxoplasma. It also provides an overview of available knowledge concerning the target proteins of parasite MAPKs and the need to understand and unravel unknown interaction network(s) of MAPK(s).
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Affiliation(s)
- Pavneet Kaur
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Neena Goyal
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India.
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14
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Horn D. Genome-scale RNAi screens in African trypanosomes. Trends Parasitol 2021; 38:160-173. [PMID: 34580035 DOI: 10.1016/j.pt.2021.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022]
Abstract
Genome-scale genetic screens allow researchers to rapidly identify the genes and proteins that impact a particular phenotype of interest. In African trypanosomes, RNA interference (RNAi) knockdown screens have revealed mechanisms underpinning drug resistance, drug transport, prodrug metabolism, quorum sensing, genome replication, and gene expression control. RNAi screening has also been remarkably effective at highlighting promising potential antitrypanosomal drug targets. The first ever RNAi library screen was implemented in African trypanosomes, and genome-scale RNAi screens and other related approaches continue to have a major impact on trypanosomatid research. Here, I review those impacts in terms of both discovery and translation.
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Affiliation(s)
- David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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15
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Marucci G, Zullino I, Bertuccini L, Camerini S, Cecchetti S, Pietrantoni A, Casella M, Vatta P, Greenwood AD, Fiorillo A, Lalle M. Re-Discovery of Giardiavirus: Genomic and Functional Analysis of Viruses from Giardia duodenalis Isolates. Biomedicines 2021; 9:654. [PMID: 34201207 PMCID: PMC8230311 DOI: 10.3390/biomedicines9060654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively studied; moreover, a positive correlation between GLV and parasite virulence is yet to be proved. To understand the biological significance of GLV infection in Giardia, the characterization of several GLV strains from naturally infected G. duodenalis isolates is necessary. Here we report high-throughput sequencing of four GLVs strains, from Giardia isolates of human and animal origin. We also report on a new, unclassified viral sequence (designed GdRV-2), unrelated to Giardiavirus, encoding and expressing for a single large protein with an RdRp domain homologous to Totiviridae and Botybirnaviridae. The result of our sequencing and proteomic analyses challenge the current knowledge on GLV and strongly suggest that viral capsid protein translation unusually starts with a proline and that translation of the RNA-dependent RNA polymerase (RdRp) occurs via a +1/-2 ribosomal frameshift mechanism. Nucleotide polymorphism, confirmed by mass-spectrometry analysis, was also observed among and between GLV strains. Phylogenetic analysis indicated the occurrence of at least two GLV subtypes which display different phenotypes and transmissibility in experimental infections of a GLV naïve Giardia isolate.
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Affiliation(s)
- Gianluca Marucci
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Ilaria Zullino
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Lucia Bertuccini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Serena Camerini
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Serena Cecchetti
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Agostina Pietrantoni
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Marialuisa Casella
- Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (L.B.); (S.C.); (S.C.); (A.P.); (M.C.)
| | - Paolo Vatta
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
| | - Alex D. Greenwood
- Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany;
- Department of Veterinary Medicine, Freie Universität Berlin, 14195 Berlin, Germany
| | - Annarita Fiorillo
- Department of Biochemical Science “A. Rossi-Fanelli”, Sapienza University, 00185 Rome, Italy;
| | - Marco Lalle
- Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (G.M.); (I.Z.); (P.V.)
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Abstract
Malaria, caused by infection with Plasmodium parasites, remains a significant global health concern. For decades, genetic intractability and limited tools hindered our ability to study essential proteins and pathways in Plasmodium falciparum, the parasite associated with the most severe malaria cases. However, recent years have seen major leaps forward in the ability to genetically manipulate P. falciparum parasites and conditionally control protein expression/function. The conditional knockdown systems used in P. falciparum target all 3 components of the central dogma, allowing researchers to conditionally control gene expression, translation, and protein function. Here, we review some of the common knockdown systems that have been adapted or developed for use in P. falciparum. Much of the work done using conditional knockdown approaches has been performed in asexual, blood-stage parasites, but we also highlight their uses in other parts of the life cycle and discuss new ways of applying these systems outside of the intraerythrocytic stages. With the use of these tools, the field’s understanding of parasite biology is ever increasing, and promising new pathways for antimalarial drug development are being discovered.
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Kirti A, Sharma M, Rani K, Bansal A. CRISPRing protozoan parasites to better understand the biology of diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:21-68. [PMID: 33934837 DOI: 10.1016/bs.pmbts.2021.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Precise gene editing techniques are paramount to gain deeper insights into the biological processes such as host-parasite interactions, drug resistance mechanisms, and gene-function relationships. Discovery of CRISPR-Cas9 system has spearheaded mechanistic understanding of protozoan parasite biology as evident from the number of reports in the last decade. Here, we have described the use of CRISPR-Cas9 in understanding the biology of medically important protozoan parasites such as Plasmodium, Leishmania, Trypanosoma, Babesia and Trichomonas. In spite of intrinsic difficulties in genome editing in these protozoan parasites, CRISPR-Cas9 has acted as a catalyst for faster generation of desired transgenic parasites. Modifications in the CRISPR-Cas9 system for improving the efficiency have been useful in better understanding the molecular mechanisms associated with repair of double strand breaks in the parasites. Moreover, improvement in reagents used for CRISPR mediated gene editing have been instrumental in addressing the issue of non-specificity and toxicity for therapeutic use. These application-based modifications may help in further increasing the efficiency of gene editing in protozoan parasites.
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Affiliation(s)
- Apurva Kirti
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manish Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Komal Rani
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhisheka Bansal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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18
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Ramos-Martínez E, Hernández-González L, Ramos-Martínez I, Pérez-Campos Mayoral L, López-Cortés GI, Pérez-Campos E, Mayoral Andrade G, Hernández-Huerta MT, José MV. Multiple Origins of Extracellular DNA Traps. Front Immunol 2021; 12:621311. [PMID: 33717121 PMCID: PMC7943724 DOI: 10.3389/fimmu.2021.621311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/06/2021] [Indexed: 01/21/2023] Open
Abstract
Extracellular DNA traps (ETs) are evolutionarily conserved antimicrobial mechanisms present in protozoa, plants, and animals. In this review, we compare their similarities in species of different taxa, and put forward the hypothesis that ETs have multiple origins. Our results are consistent with a process of evolutionary convergence in multicellular organisms through the application of a congruency test. Furthermore, we discuss why multicellularity is related to the presence of a mechanism initiating the formation of ETs.
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Affiliation(s)
- Edgar Ramos-Martínez
- School of Sciences, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | | | - Iván Ramos-Martínez
- Glycobiology, Cell Growth and Tissue Repair Research Unit (Gly-CRRET), Université Paris Est Créteil (UPEC), Créteil, France
| | - Laura Pérez-Campos Mayoral
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | | | - Eduardo Pérez-Campos
- Biochemistry and Immunology Unit, National Technological of Mexico/ITOaxaca, Oaxaca, Mexico
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | - Gabriel Mayoral Andrade
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | | | - Marco V. José
- Theoretical Biology Group, National Autonomous University of Mexico, Mexico City, Mexico
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19
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Testing the CRISPR-Cas9 and glmS ribozyme systems in Leishmania tarentolae. Mol Biochem Parasitol 2020; 241:111336. [PMID: 33166572 DOI: 10.1016/j.molbiopara.2020.111336] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 10/28/2020] [Indexed: 02/03/2023]
Abstract
Leishmania parasites include important pathogens and model organisms and are even used for the production of recombinant proteins. However, functional genomics and the characterization of essential genes are often limited in Leishmania because of low-throughput technologies for gene disruption or tagging and the absence of components for RNA interference. Here, we tested the T7 RNA polymerase-dependent CRISPR-Cas9 system by Beneke et al. and the glmS ribozyme-based knock-down system in the model parasite Leishmania tarentolae. We successfully deleted two reference genes encoding the flagellar motility factor Pf16 and the salvage-pathway enzyme adenine phosphoribosyltransferase, resulting in immotile and drug-resistant parasites, respectively. In contrast, we were unable to disrupt the gene encoding the mitochondrial flavoprotein Erv. Cultivation of L. tarentolae in standard BHI medium resulted in a constitutive down-regulation of an episomal mCherry-glmS reporter by 40 to 60%. For inducible knock-downs, we evaluated the growth of L. tarentolae in alternative media and identified supplemented MEM, IMDM and McCoy's 5A medium as candidates. Cultivation in supplemented MEM allowed an inducible, glucosamine concentration-dependent down-regulation of the episomal mCherry-glmS reporter by more than 70%. However, chromosomal glmS-tagging of the genes encoding Pf16, adenine phosphoribosyltransferase or Erv did not reveal a knock-down phenotype. Our data demonstrate the suitability of the CRISPR-Cas9 system for the disruption and tagging of genes in L. tarentolae as well as the limitations of the glmS system, which was restricted to moderate efficiencies for episomal knock-downs and caused no detectable phenotype for chromosomal knock-downs.
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20
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Rajan KS, Doniger T, Cohen-Chalamish S, Rengaraj P, Galili B, Aryal S, Unger R, Tschudi C, Michaeli S. Developmentally Regulated Novel Non-coding Anti-sense Regulators of mRNA Translation in Trypanosoma b rucei. iScience 2020; 23:101780. [PMID: 33294788 PMCID: PMC7683347 DOI: 10.1016/j.isci.2020.101780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/14/2020] [Accepted: 11/03/2020] [Indexed: 01/19/2023] Open
Abstract
The parasite Trypanosoma brucei is the causative agent of sleeping sickness and cycles between insect and mammalian hosts. The parasite appears to lack conventional transcriptional regulation of protein coding genes, and mRNAs are processed from polycistronic transcripts by the concerted action of trans-splicing and polyadenylation. Regulation of mRNA function is mediated mainly by RNA binding proteins affecting mRNA stability and translation. In this study, we describe the identification of 62 non-coding (nc) RNAs that are developmentally regulated and/or respond to stress. We characterized two novel anti-sense RNA regulators (TBsRNA-33 and 37) that originate from the rRNA loci, associate with ribosomes and polyribosomes, and interact in vivo with distinct mRNA species to regulate translation. Thus, this study suggests for the first-time anti-sense RNA regulators as an additional layer for controlling gene expression in these parasites. Trypanosome non-coding RNAs (ncRNAs) are developmentally regulated during cycling between two hosts ncRNAs originate from rRNA locus and associate with the ribosome en route to cytoplasm In vivo cross-linking enable identification of target RNA species regulated by ncRNAs Trypanosomes possess anti-sense ncRNAs that regulate translation
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Affiliation(s)
- K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Praveenkumar Rengaraj
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Beathrice Galili
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Saurav Aryal
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
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21
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Cárdenas-Guerra RE, Moreno-Gutierrez DS, Vargas-Dorantes ODJ, Espinoza B, Hernandez-Garcia A. Delivery of Antisense DNA into Pathogenic Parasite Trypanosoma cruzi Using Virus-Like Protein-Based Nanoparticles. Nucleic Acid Ther 2020; 30:392-401. [PMID: 32907491 DOI: 10.1089/nat.2020.0870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Trypanosoma cruzi, which causes Chagas disease, is one of the most lacerating parasites in terms of health and social impacts. New approaches for its study and treatment are urgently needed since in more than 50 years only two drugs have been approved. Genetic approaches based on antisense oligonucleotides (AONs) are promising; however, to harness their full potential the development of effective carriers is paramount. Here, we report the use of an engineered virus-like protein C-BK12 to transfect AONs into T. cruzi. Using gel electrophoresis, Dynamic Light Scattering, and atomic force microscopy, we found that C-BK12 binds AONs and forms 10-25 nm nanoparticles (NPs), which are very stable when incubated in biological media, only releasing up to 25% of AON. Fluorescence microscopy and qPCR revealed that the NPs successfully delivered AONs into epimastigotes and reduced the expression of a target gene down to 68%. Importantly, the protein did not show cytotoxicity. The combination of high stability and capability to transfect and knock down gene expression without causing cell damage and death makes the protein C-BK12 a promising starting point for the further development of safe and effective carriers to deliver AONs into T. cruzi for biological studies.
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Affiliation(s)
- Rosa E Cárdenas-Guerra
- Laboratorio de Estudios sobre Tripanosomiasis, Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - David S Moreno-Gutierrez
- Laboratory of Biomolecular Engineering and Bionanotechnology, Departamento de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Oscar de J Vargas-Dorantes
- Laboratory of Biomolecular Engineering and Bionanotechnology, Departamento de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Bertha Espinoza
- Laboratorio de Estudios sobre Tripanosomiasis, Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Armando Hernandez-Garcia
- Laboratory of Biomolecular Engineering and Bionanotechnology, Departamento de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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Yagoubat A, Corrales RM, Bastien P, Lévêque MF, Sterkers Y. Gene Editing in Trypanosomatids: Tips and Tricks in the CRISPR-Cas9 Era. Trends Parasitol 2020; 36:745-760. [DOI: 10.1016/j.pt.2020.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/19/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022]
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Qasim M, Xiao H, He K, Omar MAA, Liu F, Ahmed S, Li F. Genetic engineering and bacterial pathogenesis against the vectorial capacity of mosquitoes. Microb Pathog 2020; 147:104391. [PMID: 32679245 DOI: 10.1016/j.micpath.2020.104391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/05/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022]
Abstract
Mosquitoes are the main vector of multiple diseases worldwide and transmit viral (malaria, chikungunya, encephalitis, yellow fever, as well as dengue fever), as well as bacterial diseases (tularemia). To manage the outbreak of mosquito populations, various management programs include the application of chemicals, followed by biological and genetic control. Here we aimed to focus on the role of bacterial pathogenesis and molecular tactics for the management of mosquitoes and their vectorial capacity. Bacterial pathogenesis and molecular manipulations have a substantial impact on the biology of mosquitoes, and both strategies change the gene expression and regulation of disease vectors. The strategy for genetic modification is also proved to be excellent for the management of mosquitoes, which halt the development of population via incompatibility of different sex. Therefore, the purpose of the present discussion is to illustrate the impact of both approaches against the vectorial capacity of mosquitoes. Moreover, it could be helpful to understand the relationship of insect-pathogen and to manage various insect vectors as well as diseases.
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Affiliation(s)
- Muhammad Qasim
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Huamei Xiao
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China; College of Life Sciences and Resource Environment, Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, Yichun University, Yichun, 336000, China
| | - Kang He
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mohamed A A Omar
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Feiling Liu
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Sohail Ahmed
- Department of Entomology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Fei Li
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Abstract
The parasites of the genus Cryptosporidium are important causes of diarrheal diseases, specifically cryptosporidiosis, worldwide. A major bottleneck for developing drugs and vaccines against cryptosporidiosis is the lack of methods to study gene function in this parasite. Silencing of genes by RNA interference (RNAi) is a powerful method to investigate gene function that has been widely used in the identification of targets for several pathogens. Unfortunately, as Cryptosporidium does not possess the enzymes of the RNAi pathway, its genes cannot be silenced by standard siRNA technology. To circumvent that problem, we have developed a novel strategy to knock down Cryptosporidium genes by reconstituting the effector arm of the siRNA pathway. We have induced silencing of several genes in Cryptosporidium by transfecting parasites with hybrid complexes formed between recombinant human Argonaute (hAgo2) and Cryptosporidium single-stranded RNA (ssRNA). This novel methodology provides an effective strategy to study the role of selected genes in host-parasite interactions, and also can be used to identify potential targets for chemotherapy. The standardized methodology based on this strategy is described in this chapter.
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Abstract
Leishmania parasites are the causative agents of a broad spectrum of diseases. The parasites migrate between sand-fly vectors and mammalian hosts, adapting to changing environments by driving a regulated program of gene expression, with translation regulation playing a key role. The leishmanias encode six different paralogs of eIF4E, the cap-binding translation initiation factor. Since these vary in function, expression profile, and assemblage, it is assumed that each is assigned a specific role throughout the life cycle. Using the CRISPR-Cas9 system for Leishmania, we generated a null mutant of LeishIF4E1, eliminating both alleles. Although the mutant cells were viable, their morphology was altered and their ability to synthesize the flagellum was impaired. Elimination of LeishIF4E1 affected their protein expression profile and decreased their ability to infect cultured macrophages. Restoring LeishIF4E1 expression restored the affected features. This study highlights the importance of LeishIF4E1 in diverse cellular events during the life cycle of Leishmania. Leishmania parasites cycle between sand-fly vectors and mammalian hosts, adapting to changing environmental conditions by driving a stage-specific program of gene expression, which is tightly regulated by translation processes. Leishmania encodes six eIF4E orthologs (LeishIF4Es) and five eIF4G candidates, forming different cap-binding complexes with potentially varying functions. Most LeishIF4E paralogs display temperature sensitivity in their cap-binding activity, except for LeishIF4E1, which maintains its cap-binding activity under all conditions. We used the CRISPR-Cas9 system to successfully generate a null mutant of LeishIF4E1 and examine how its elimination affected parasite physiology. Although the LeishIF4E1–/– null mutant was viable, its growth was impaired, in line with a reduction in global translation. As a result of the mutation, the null LeishIF4E1–/– mutant had a defective morphology, as the cells were round and unable to grow a normal flagellum. This was further emphasized when the LeishIF4E1–/– cells failed to develop the promastigote morphology once they shifted from conditions that generate axenic amastigotes (33°C, pH 5.5) back to neutral pH and 25°C, and they maintained their short flagellum and circular structure. Finally, the LeishIF4E1–/– null mutant displayed difficulty in infecting cultured macrophages. The morphological changes and reduced infectivity of the mutant may be related to differences in the proteomic profile of LeishIF4E1–/– cells from that of controls. All defects monitored in the LeishIF4E1–/– null mutant were reversed in the add-back strain, in which expression of LeishIF4E1 was reconstituted, establishing a strong link between the cellular defects and the absence of LeishIF4E1 expression. IMPORTANCELeishmania parasites are the causative agents of a broad spectrum of diseases. The parasites migrate between sand-fly vectors and mammalian hosts, adapting to changing environments by driving a regulated program of gene expression, with translation regulation playing a key role. The leishmanias encode six different paralogs of eIF4E, the cap-binding translation initiation factor. Since these vary in function, expression profile, and assemblage, it is assumed that each is assigned a specific role throughout the life cycle. Using the CRISPR-Cas9 system for Leishmania, we generated a null mutant of LeishIF4E1, eliminating both alleles. Although the mutant cells were viable, their morphology was altered and their ability to synthesize the flagellum was impaired. Elimination of LeishIF4E1 affected their protein expression profile and decreased their ability to infect cultured macrophages. Restoring LeishIF4E1 expression restored the affected features. This study highlights the importance of LeishIF4E1 in diverse cellular events during the life cycle of Leishmania.
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Functional Characterization of Entamoeba histolytica Argonaute Proteins Reveals a Repetitive DR-Rich Motif Region That Controls Nuclear Localization. mSphere 2019; 4:4/5/e00580-19. [PMID: 31619501 PMCID: PMC6796981 DOI: 10.1128/msphere.00580-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The RNA interference (RNAi) pathway regulates gene expression in many eukaryotic organisms. Argonaute (Ago) proteins, together with bound small RNAs (sRNAs), are key effectors that mediate gene silencing function. However, there is limited knowledge of Ago proteins and their functions in nonmodel systems. In the protozoan parasite Entamoeba histolytica, RNAi is a robust means for stable gene silencing mediated via large populations of antisense sRNAs. Here, we report functional characterization of three Ago proteins in E. histolytica (EhAgo2-1, EhAgo2-2, and EhAgo2-3). Our data show that each EhAgo protein has a distinct subcellular localization and binds 27-nucleotide (nt) sRNAs and that the localization of EhAgo proteins is altered in response to stress conditions. Via mutagenesis analyses, we demonstrated that the Ago PAZ (Piwi/Argonaute/Zwille) domain in all three EhAgos is essential for sRNA binding. With mutation of the PAZ domain in EhAgo2-2, there was no effect on the nuclear localization of the protein but a strong phenotype and a growth defect. We further show that EhAgo2-2 contains an unusual repetitive DR-rich (aspartic acid, arginine-rich) motif region which functions as a nuclear localization signal (NLS) and is both necessary and sufficient to mediate nuclear localization. Overall, our data delineate the localization and sRNA binding features of the three E. histolytica Ago proteins and demonstrate that the PAZ domain is necessary for sRNA binding. The repetitive DR-rich motif region in EhAgo2-2 has not previously been defined in other systems, which adds to the novel observations that can be made when studies of the RNAi pathway are extended to nonmodel systems.IMPORTANCE The protozoan parasite Entamoeba histolytica, which causes amebiasis and affects over 50 million people worldwide, contains an important RNAi pathway for gene silencing. Gene silencing via the RNAi pathway is mediated by the Argonaute (Ago) proteins. However, we lack knowledge on Ago function(s) in this nonmodel system. In this paper, we discovered that three E. histolytica Ago proteins (EhAgo2-1, EhAgo2-2, and EhAgo2-3) all bind 27-nt small RNAs and have distinct subcellular localizations, which change in response to stress conditions. The EhAgos bind small RNA populations via their PAZ domains. An unusual repetitive DR-rich motif region is identified in EhAgo2-2 that functions as a nuclear localization signal. Our results show for the first time an active nuclear transport process of the EhAgo2-2 RNA-induced silencing complex (RISC) in this parasite. These data add to the novel observations that can be made when studies of the RNAi pathway are extended to nonmodel systems.
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Shapiro RS, Chavez A, Collins JJ. CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat Rev Microbiol 2019; 16:333-339. [PMID: 29599458 DOI: 10.1038/s41579-018-0002-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genetic manipulation of microorganisms has been crucial in understanding their biology, yet for many microbial species, robust tools for comprehensive genetic analysis were lacking until the advent of CRISPR-Cas-based gene editing techniques. In this Progress article, we discuss advances in CRISPR-based techniques for the genetic analysis of genetically intractable microorganisms, with an emphasis on mycobacteria, fungi and parasites. We discuss how CRISPR-based analyses in these organisms have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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Lander N, Chiurillo MA. State-of-the-art CRISPR/Cas9 Technology for Genome Editing in Trypanosomatids. J Eukaryot Microbiol 2019; 66:981-991. [PMID: 31211904 DOI: 10.1111/jeu.12747] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/23/2022]
Abstract
CRISPR/Cas9 technology has revolutionized biology. This prokaryotic defense system against foreign DNA has been repurposed for genome editing in a broad range of cell tissues and organisms. Trypanosomatids are flagellated protozoa belonging to the order Kinetoplastida. Some of its most representative members cause important human diseases affecting millions of people worldwide, such as Chagas disease, sleeping sickness and different forms of leishmaniases. Trypanosomatid infections represent an enormous burden for public health and there are no effective treatments for most of the diseases they cause. Since the emergence of the CRISPR/Cas9 technology, the genetic manipulation of these parasites has notably improved. As a consequence, genome editing is now playing a key role in the functional study of proteins, in the characterization of metabolic pathways, in the validation of alternative targets for antiparasitic interventions, and in the study of parasite biology and pathogenesis. In this work we review the different strategies that have been used to adapt the CRISPR/Cas9 system to Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp., as well as the research progress achieved using these approaches. Thereby, we will present the state-of-the-art molecular tools available for genome editing in trypanosomatids to finally point out the future perspectives in the field.
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Affiliation(s)
- Noelia Lander
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602
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Osorio-Méndez JF, Cevallos AM. Discovery and Genetic Validation of Chemotherapeutic Targets for Chagas' Disease. Front Cell Infect Microbiol 2019; 8:439. [PMID: 30666299 PMCID: PMC6330712 DOI: 10.3389/fcimb.2018.00439] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023] Open
Abstract
There is an urgent need to develop new treatments for Chagas' disease. To identify drug targets, it is important to understand the basic biology of Trypanosoma cruzi, in particular with respect to the biological pathways or proteins that are essential for its survival within the host. This review provides a streamlined approach for identifying drug targets using freely available chemogenetic databases and outlines the relevant characteristics of an ideal chemotherapeutic target. Among those are their essentiality, druggability, availability of structural information, and selectivity. At the moment only 16 genes have been found as essential by gene disruption in T. cruzi. At the TDR Targets database, a chemogenomics resource for neglected diseases, information about published structures for these genes was only found for three of these genes, and annotation of validated inhibitors was found in two. These inhibitors have activity against the parasitic stages present in the host. We then analyzed three of the pathways that are considered promising in the search for new targets: (1) Ergosterol biosynthesis, (2) Resistance to oxidative stress, (3) Synthesis of surface glycoconjugates. We have annotated all the genes that participate in them, identified those that are considered as druggable, and incorporated evidence from either Trypanosoma brucei, and Leishmania spp. that supports the hypothesis that these pathways are essential for T. cruzi survival.
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Affiliation(s)
- Juan Felipe Osorio-Méndez
- Laboratorio de Microbiología y Biología Molecular, Programa de Medicina, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia, Colombia.,Grupo de Estudio en Parasitología Molecular, Centro de Investigaciones Biomédicas, Universidad del Quindío, Armenia, Colombia
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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McDonald L, Cayla M, Ivens A, Mony BM, MacGregor P, Silvester E, McWilliam K, Matthews KR. Non-linear hierarchy of the quorum sensing signalling pathway in bloodstream form African trypanosomes. PLoS Pathog 2018; 14:e1007145. [PMID: 29940034 PMCID: PMC6034907 DOI: 10.1371/journal.ppat.1007145] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/06/2018] [Accepted: 06/07/2018] [Indexed: 01/23/2023] Open
Abstract
Trypanosoma brucei, the agents of African trypanosomiasis, undergo density-dependent differentiation in the mammalian bloodstream to prepare for transmission by tsetse flies. This involves the generation of cell-cycle arrested, quiescent, stumpy forms from proliferative slender forms. The signalling pathway responsible for the quorum sensing response has been catalogued using a genome-wide selective screen, providing a compendium of signalling protein kinases phosphatases, RNA binding proteins and hypothetical proteins. However, the ordering of these components is unknown. To piece together these components to provide a description of how stumpy formation arises we have used an extragenic suppression approach. This exploited a combinatorial gene knockout and overexpression strategy to assess whether the loss of developmental competence in null mutants of pathway components could be compensated by ectopic expression of other components. We have created null mutants for three genes in the stumpy induction factor signalling pathway (RBP7, YAK, MEKK1) and evaluated complementation by expression of RBP7, NEK17, PP1-6, or inducible gene silencing of the proposed differentiation inhibitor TbTOR4. This indicated that the signalling pathway is non-linear. Phosphoproteomic analysis focused on one pathway component, a putative MEKK, identified molecules with altered expression and phosphorylation profiles in MEKK1 null mutants, including another component in the pathway, NEK17. Our data provide a first molecular dissection of multiple components in a signal transduction cascade in trypanosomes.
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Affiliation(s)
- Lindsay McDonald
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Mathieu Cayla
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Binny M. Mony
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Paula MacGregor
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsty McWilliam
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Keith R. Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Expanding the toolbox for Trypanosoma cruzi: A parasite line incorporating a bioluminescence-fluorescence dual reporter and streamlined CRISPR/Cas9 functionality for rapid in vivo localisation and phenotyping. PLoS Negl Trop Dis 2018; 12:e0006388. [PMID: 29608569 PMCID: PMC5897030 DOI: 10.1371/journal.pntd.0006388] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/12/2018] [Accepted: 03/14/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Infection with Trypanosoma cruzi causes Chagas disease, a major public health problem throughout Latin America. There is no vaccine and the only drugs have severe side effects. Efforts to generate new therapies are hampered by limitations in our understanding of parasite biology and disease pathogenesis. Studies are compromised by the complexity of the disease, the long-term nature of the infection, and the fact that parasites are barely detectable during the chronic stage. In addition, functional dissection of T. cruzi biology has been restricted by the limited flexibility of the genetic manipulation technology applicable to this parasite. METHODOLOGY/PRINCIPAL FINDINGS Here, we describe two technical innovations, which will allow the role of the parasite in disease progression to be better assessed. First, we generated a T. cruzi reporter strain that expresses a fusion protein comprising red-shifted luciferase and green fluorescent protein domains. Bioluminescence allows the kinetics of infection to be followed within a single animal, and specific foci of infection to be pinpointed in excised tissues. Fluorescence can then be used to visualise individual parasites in tissue sections to study host-parasite interactions at a cellular level. Using this strategy, we have been routinely able to find individual parasites within chronically infected murine tissues for the first time. The second advance is the incorporation of a streamlined CRISPR/Cas9 functionality into this reporter strain that can facilitate genome editing using a PCR-based approach that does not require DNA cloning. This system allows the rapid generation of null mutants and fluorescently tagged parasites in a background where the in vivo phenotype can be rapidly assessed. CONCLUSIONS/SIGNIFICANCE The techniques described here will have multiple applications for studying aspects of T. cruzi biology and Chagas disease pathogenesis previously inaccessible to conventional approaches. The reagents and cell lines have been generated as a community resource and are freely available on request.
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Stroehlein AJ, Young ND, Gasser RB. Advances in kinome research of parasitic worms - implications for fundamental research and applied biotechnological outcomes. Biotechnol Adv 2018; 36:915-934. [PMID: 29477756 DOI: 10.1016/j.biotechadv.2018.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022]
Abstract
Protein kinases are enzymes that play essential roles in the regulation of many cellular processes. Despite expansions in the fields of genomics, transcriptomics and bioinformatics, there is limited information on the kinase complements (kinomes) of most eukaryotic organisms, including parasitic worms that cause serious diseases of humans and animals. The biological uniqueness of these worms and the draft status of their genomes pose challenges for the identification and classification of protein kinases using established tools. In this article, we provide an account of kinase biology, the roles of kinases in diseases and their importance as drug targets, and drug discovery efforts in key socioeconomically important parasitic worms. In this context, we summarise methods and resources commonly used for the curation, identification, classification and functional annotation of protein kinase sequences from draft genomes; review recent advances made in the characterisation of the worm kinomes; and discuss the implications of these advances for investigating kinase signalling and developing small-molecule inhibitors as new anti-parasitic drugs.
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Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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RNAi-Mediated Specific Gene Silencing as a Tool for the Discovery of New Drug Targets in Giardia lamblia; Evaluation Using the NADH Oxidase Gene. Genes (Basel) 2017; 8:genes8110303. [PMID: 29099754 PMCID: PMC5704216 DOI: 10.3390/genes8110303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/12/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022] Open
Abstract
The microaerophilic protozoan Giardia lamblia is the agent causing giardiasis, an intestinal parasitosis of worldwide distribution. Different pharmacotherapies have been employed against giardiasis; however, side effects in the host and reports of drug resistant strains generate the need to develop new strategies that identify novel biological targets for drug design. To support this requirement, we have designed and evaluated a vector containing a cassette for the synthesis of double-stranded RNA (dsRNA), which can silence expression of a target gene through the RNA interference (RNAi) pathway. Small silencing RNAs were detected and quantified in transformants expressing dsRNA by a stem-loop RT-qPCR approach. The results showed that, in transformants expressing dsRNA of 100-200 base pairs, the level of NADHox mRNA was reduced by around 30%, concomitant with a decrease in enzyme activity and a reduction in the number of trophozoites with respect to the wild type strain, indicating that NADHox is indeed an important enzyme for Giardia viability. These results suggest that it is possible to induce the G. lamblia RNAi machinery for attenuating the expression of genes encoding proteins of interest. We propose that our silencing strategy can be used to identify new potential drug targets, knocking down genes encoding different structural proteins and enzymes from a wide variety of metabolic pathways.
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Duncan SM, Jones NG, Mottram JC. Recent advances in Leishmania reverse genetics: Manipulating a manipulative parasite. Mol Biochem Parasitol 2017. [DOI: 10.1016/j.molbiopara.2017.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Characterization of the Protein Tyrosine Phosphatase LmPRL-1 Secreted by Leishmania major via the Exosome Pathway. Infect Immun 2017; 85:IAI.00084-17. [PMID: 28507071 DOI: 10.1128/iai.00084-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/11/2017] [Indexed: 01/02/2023] Open
Abstract
Similar to other intracellular pathogens, Leishmania parasites are known to evade the antimicrobial effector functions of host immune cells. To date, however, only a few virulence factors have been described for Leishmania major, one of the causative agents of cutaneous leishmaniasis. Here, we have characterized the expression and function of an L. major phosphatase, which we termed LmPRL-1. This enzyme shows a strong structural similarity to the human phosphatases of regenerating liver (PRL-1, -2, and -3) that regulate the proliferation, differentiation, and motility of cells. The biochemical characterization of the L. major phosphatase revealed that the enzyme is redox sensitive. When analyzing the subcellular localization of LmPRL-1 in promastigotes, amastigotes, and infected macrophages, we found that the phosphatase was predominantly expressed and secreted by promastigotes via the exosome route. Finally, we observed that ectopic expression of LmPRL-1 in L. major led to an increased number of parasites in macrophages. From these data, we conclude that the L. major phosphatase LmPRL-1 contributes to the intracellular survival of the parasites in macrophages.
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Tarique M, Chauhan M, Tuteja R. ATPase activity of Plasmodium falciparum MLH is inhibited by DNA-interacting ligands and dsRNAs of MLH along with UvrD curtail malaria parasite growth. PROTOPLASMA 2017; 254:1295-1305. [PMID: 27624787 DOI: 10.1007/s00709-016-1021-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Malaria caused by Plasmodium falciparum is the major disease burden all over the world. Recently, the situation has deteriorated because the malarial parasites are becoming progressively more resistant to numerous commonly used antimalarial drugs. Thus, there is a critical requirement to find other means to restrict and eliminate malaria. The mismatch repair (MMR) machinery of parasite is quite unique in several ways, and it can be exploited for finding new drug targets. MutL homolog (MLH) is one of the major components of MMR machinery, and along with UvrD, it helps in unwinding the DNA. We have screened several DNA-interacting ligands for their effect on intrinsic ATPase activity of PfMLH protein. This screening suggested that several ligands such as daunorubicin, etoposide, ethidium bromide, netropsin, and nogalamycin are inhibitors of the ATPase activity of PfMLH, and their apparent IC50 values range from 2.1 to 9.35 μM. In the presence of nogalamycin and netropsin, the effect was significant because in their presence, the V max value dropped from 1.024 μM of hydrolyzed ATP/min to 0.596 and 0.643 μM of hydrolyzed ATP/min, respectively. The effect of double-stranded RNAs of PfMLH and PfUvrD on growth of P. falciparum 3D7 strain was studied. The parasite growth was significantly inhibited suggesting that these components belonging to MMR pathway are crucial for the survival of the parasite.
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Affiliation(s)
- Mohammed Tarique
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manish Chauhan
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Renu Tuteja
- Parasite Biology Group, International Centre for Genetic Engineering and Biotechnology, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Bayer-Santos E, Marini MM, da Silveira JF. Non-coding RNAs in Host-Pathogen Interactions: Subversion of Mammalian Cell Functions by Protozoan Parasites. Front Microbiol 2017; 8:474. [PMID: 28377760 PMCID: PMC5359270 DOI: 10.3389/fmicb.2017.00474] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/08/2017] [Indexed: 01/23/2023] Open
Abstract
Pathogens have evolved mechanisms to modulate host cell functions and avoid recognition and destruction by the host damage response. For many years, researchers have focused on proteins as the main effectors used by pathogens to hijack host cell pathways, but only recently with the development of deep RNA sequencing these molecules were brought to light as key players in infectious diseases. Protozoan parasites such as those from the genera Plasmodium, Toxoplasma, Leishmania, and Trypanosoma cause life-threatening diseases and are responsible for 1000s of deaths worldwide every year. Some of these parasites replicate intracellularly when infecting mammalian hosts, whereas others can survive and replicate extracellularly in the bloodstream. Each of these parasites uses specific evasion mechanisms to avoid being killed by the host defense system. An increasing number of studies have shown that these pathogens can transfer non-coding RNA molecules to the host cells to modulate their functions. This transference usually happens via extracellular vesicles, which are small membrane vesicles secreted by the microorganism. In this mini-review we will combine published work regarding several protozoan parasites that were shown to use non-coding RNAs in inter-kingdom communication and briefly discuss future perspectives in the field.
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Affiliation(s)
- Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo São Paulo, Brazil
| | - Marjorie M Marini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
| | - José F da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo São Paulo, Brazil
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Bittencourt IDA, Serpeloni M, Hiraiwa PM, de Arruda Campos Brasil de Souza T, Ávila AR. Dissecting biochemical peculiarities of the ATPase activity of TcSub2, a component of the mRNA export pathway in Trypanosoma cruzi. Int J Biol Macromol 2017; 98:793-801. [PMID: 28212935 DOI: 10.1016/j.ijbiomac.2017.02.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 11/16/2022]
Abstract
The RNA helicase DEAD-box protein Sub2 (yeast)/UAP56 (mammals) is conserved across eukaryotes and is essential for mRNA export in trypanosomes. Despite the high conservation of Sub2 in lower eukaryotes such as Trypanosoma cruzi, the low conservation of other mRNA export factors raises questions regarding whether the mode of action of TcSub2 is similar to that of orthologs from other eukaryotes. Mutation of the conserved K87 residue of TcSub2 abolishes ATPase activity, showing that its ATPase domain is functional. However, the Vmax of TcSub2 was much higher than the Vmax described for the human protein UAP56, which suggests that the TcSub2 enzyme hydrolyzes ATP faster than its human homolog. Furthermore, we demonstrate that RNA association is less important to the activity of TcSub2 compared to UAP56. Our results show differences in activity of this protein, even though the structure of TcSub2 is very similar to UAP56. Functional complementation assays indicate that these differences may be common to other trypanosomatids. Distinct features of RNA influence and ATPase efficiency between UAP56 and TcSub2 may reflect distinct structures for functional sites of TcSub2. For this reason, ligand-based or structure-based methodologies can be applied to investigate the potential of TcSub2 as a target for new drugs.
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Tools for attenuation of gene expression in malaria parasites. Int J Parasitol 2017; 47:385-398. [PMID: 28153780 DOI: 10.1016/j.ijpara.2016.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 11/28/2016] [Indexed: 12/30/2022]
Abstract
An understanding of the biology of Plasmodium parasites, which are the causative agents of the disease malaria, requires study of gene function. Various reverse genetic tools have been described for determining gene function. These tools can be broadly grouped as trans- and cis-acting. Trans-acting tools control gene functions through synthetic nucleic acid probe molecules matching the sequence of the gene of interest. Once delivered to the parasite, the probe engages with the mRNA of the target gene and attenuates its function. Cis-acting tools control gene function through elements introduced into the gene of interest by DNA transfection. The expression of the modified gene can be controlled using external agents, typically small molecule ligands. In this review, we discuss the strengths and weaknesses of these tools to guide researchers in selecting the appropriate tool for studies of gene function, and for guiding future refinements of these tools.
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Gene silencing of Dim-1, a member of the disorganized muscle family, in Haemonchus contortus. Mol Biochem Parasitol 2017; 211:71-74. [DOI: 10.1016/j.molbiopara.2016.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/19/2022]
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Stem-Loop RT-qPCR as an Efficient Tool for the Detection and Quantification of Small RNAs in Giardia lamblia. Genes (Basel) 2016; 7:genes7120131. [PMID: 27999395 PMCID: PMC5192507 DOI: 10.3390/genes7120131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 11/16/2022] Open
Abstract
Stem-loop quantitative reverse transcription PCR (RT-qPCR) is a molecular technique used for identification and quantification of individual small RNAs in cells. In this work, we used a Universal ProbeLibrary (UPL)-based design to detect-in a rapid, sensitive, specific, and reproducible way-the small nucleolar RNA (snoRNA) GlsR17 and its derived miRNA (miR2) of Giardia lamblia using a stem-loop RT-qPCR approach. Both small RNAs could be isolated from both total RNA and small RNA samples. Identification of the two small RNAs was carried out by sequencing the PCR-amplified small RNA products upon ligation into the pJET1.2/blunt vector. GlsR17 is constitutively expressed during the 72 h cultures of trophozoites, while the mature miR2 is present in 2-fold higher abundance during the first 48 h than at 72 h. Because it has been suggested that miRNAs in G. lamblia have an important role in the regulation of gene expression, the use of the stem-loop RT-qPCR method could be valuable for the study of miRNAs of G. lamblia. This methodology will be a powerful tool for studying gene regulation in G. lamblia, and will help to better understand the features and functions of these regulatory molecules and how they work within the RNA interference (RNAi) pathway in G. lamblia.
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Beltrame-Botelho IT, Talavera-López C, Andersson B, Grisard EC, Stoco PH. A Comparative In Silico Study of the Antioxidant Defense Gene Repertoire of Distinct Lifestyle Trypanosomatid Species. Evol Bioinform Online 2016; 12:263-275. [PMID: 27840574 PMCID: PMC5100842 DOI: 10.4137/ebo.s40648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/05/2016] [Accepted: 10/11/2016] [Indexed: 12/24/2022] Open
Abstract
Kinetoplastids are an ancestral group of protists that contains free-living species and parasites with distinct mechanisms in response to stress. Here, we compared genes involved in antioxidant defense (AD), proposing an evolution model among trypanosomatids. All genes were identified in Bodo saltans, suggesting that AD mechanisms have evolved prior to adaptation for parasitic lifestyles. While most of the monoxenous and dixenous parasites revealed minor differences from B. saltans, the endosymbiont-bearing species have an increased number of genes. The absence of these genes was mainly observed in the extracellular parasites of the genera Phytomonas and Trypanosoma. In trypanosomes, a distinction was observed between stercorarian and salivarian parasites, except for Trypanosoma rangeli. Our analyses indicate that the variability of AD among trypanosomatids at the genomic level is not solely due to the geographical isolation, being mainly related to specific adaptations of their distinct biological cycles within insect vectors and to a parasitism of a wide range of hosts.
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Affiliation(s)
- Ingrid Thaís Beltrame-Botelho
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
- Universidade do Sul de Santa Catarina, Palhoça, SC, Brazil
| | | | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Edmundo Carlos Grisard
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Patricia Hermes Stoco
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
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Catta-Preta CMC, Dos Santos Pascoalino B, de Souza W, Mottram JC, Motta MCM, Schenkman S. Reduction of Tubulin Expression in Angomonas deanei by RNAi Modifies the Ultrastructure of the Trypanosomatid Protozoan and Impairs Division of Its Endosymbiotic Bacterium. J Eukaryot Microbiol 2016; 63:794-803. [PMID: 27194398 DOI: 10.1111/jeu.12326] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/03/2016] [Accepted: 05/11/2016] [Indexed: 12/18/2022]
Abstract
In the last two decades, RNA interference pathways have been employed as a useful tool for reverse genetics in trypanosomatids. Angomonas deanei is a nonpathogenic trypanosomatid that maintains an obligatory endosymbiosis with a bacterium related to the Alcaligenaceae family. Studies of this symbiosis can help us to understand the origin of eukaryotic organelles. The recent elucidation of both the A. deanei and the bacterium symbiont genomes revealed that the host protozoan codes for the enzymes necessary for RNAi activity in trypanosomatids. Here, we tested the functionality of the RNAi machinery by transfecting cells with dsRNA to a reporter gene (green fluorescent protein), which had been previously expressed in the parasite and to α-tubulin, an endogenous gene. In both cases, protein expression was reduced by the presence of specific dsRNA, inducing, respectively, a decreased GFP fluorescence and the formation of enlarged cells with modified arrangement of subpellicular microtubules. Furthermore, symbiont division was impaired. These results indicate that the RNAi system is active in A. deanei and can be used to further explore gene function in symbiont-containing trypanosomatids and to clarify important aspects of symbiosis and cell evolution.
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Affiliation(s)
- Carolina Moura Costa Catta-Preta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, bloco G/SS, 21949-900, Rio de Janeiro, RJ, Brazil.,Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, United Kingdom.,Department of Biology, Centre for Immunology and Infection, University of York, York, YO10 5DD, United Kingdom
| | - Bruno Dos Santos Pascoalino
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Pedro de Toledo 669, L6A, 04039-032, São Paulo, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, bloco G/SS, 21949-900, Rio de Janeiro, RJ, Brazil
| | - Jeremy C Mottram
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, United Kingdom.,Department of Biology, Centre for Immunology and Infection, University of York, York, YO10 5DD, United Kingdom
| | - Maria Cristina M Motta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, bloco G/SS, 21949-900, Rio de Janeiro, RJ, Brazil.
| | - Sergio Schenkman
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Pedro de Toledo 669, L6A, 04039-032, São Paulo, Brazil.
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Aphasizheva I, Zhang L, Aphasizhev R. Investigating RNA editing factors from trypanosome mitochondria. Methods 2016; 107:23-33. [PMID: 27020893 PMCID: PMC5094665 DOI: 10.1016/j.ymeth.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial U-insertion/deletion mRNA editing is carried out by two principal multiprotein assemblies, enzymatic RNA editing core (RECC) and RNA editing substrate binding (RESC) complexes, and a plethora of auxiliary factors. An integral part of mitochondrial gene expression, editing receives inputs from primary mRNA and gRNA precursor processing pathways, and generates substrates for mRNA polyadenylation and translation. Although nearly all RECC-embedded enzymes have been implicated in specific editing reactions, the majority of proteins that populate the RESC are also essential for generating edited mRNAs. However, lack of recognizable motifs in RESC subunits limits the prowess of bioinformatics in guiding biochemical experiments and elucidating their specific biological functions. In this chapter, we describe a generic workflow for investigating mitochondrial mRNA editing in Trypanosoma brucei and focus on several methods that proved instrumental is assigning definitive functions to editing factors lacking known signature sequences.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA.
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
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Sanchez MA, Tran KD, Valli J, Hobbs S, Johnson E, Gluenz E, Landfear SM. KHARON Is an Essential Cytoskeletal Protein Involved in the Trafficking of Flagellar Membrane Proteins and Cell Division in African Trypanosomes. J Biol Chem 2016; 291:19760-73. [PMID: 27489106 DOI: 10.1074/jbc.m116.739235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 11/06/2022] Open
Abstract
African trypanosomes and related kinetoplastid parasites selectively traffic specific membrane proteins to the flagellar membrane, but the mechanisms for this trafficking are poorly understood. We show here that KHARON, a protein originally identified in Leishmania parasites, interacts with a putative trypanosome calcium channel and is required for its targeting to the flagellar membrane. KHARON is located at the base of the flagellar axoneme, where it likely mediates targeting of flagellar membrane proteins, but is also on the subpellicular microtubules and the mitotic spindle. Hence, KHARON is probably a multifunctional protein that associates with several components of the trypanosome cytoskeleton. RNA interference-mediated knockdown of KHARON mRNA results in failure of the calcium channel to enter the flagellar membrane, detachment of the flagellum from the cell body, and disruption of mitotic spindles. Furthermore, knockdown of KHARON mRNA induces a lethal failure of cytokinesis in both bloodstream (mammalian host) and procyclic (insect vector) life cycle stages, and KHARON is thus critical for parasite viability.
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Affiliation(s)
- Marco A Sanchez
- From the Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239 and
| | - Khoa D Tran
- From the Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239 and
| | - Jessica Valli
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Sam Hobbs
- From the Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239 and
| | - Errin Johnson
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Eva Gluenz
- the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Scott M Landfear
- From the Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239 and
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Lander N, Chiurillo MA, Docampo R. Genome Editing by CRISPR/Cas9: A Game Change in the Genetic Manipulation of Protists. J Eukaryot Microbiol 2016; 63:679-90. [PMID: 27315329 DOI: 10.1111/jeu.12338] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/12/2016] [Accepted: 06/13/2016] [Indexed: 01/01/2023]
Abstract
Genome editing by CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated gene 9) system has been transformative in biology. Originally discovered as an adaptive prokaryotic immune system, CRISPR/Cas9 has been repurposed for genome editing in a broad range of model organisms, from yeast to mammalian cells. Protist parasites are unicellular organisms producing important human diseases that affect millions of people around the world. For many of these diseases, such as malaria, Chagas disease, leishmaniasis and cryptosporidiosis, there are no effective treatments or vaccines available. The recent adaptation of the CRISPR/Cas9 technology to several protist models will be playing a key role in the functional study of their proteins, in the characterization of their metabolic pathways, and in the understanding of their biology, and will facilitate the search for new chemotherapeutic targets. In this work we review recent studies where the CRISPR/Cas9 system was adapted to protist parasites, particularly to Apicomplexans and trypanosomatids, emphasizing the different molecular strategies used for genome editing of each organism, as well as their advantages. We also discuss the potential usefulness of this technology in the green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Noelia Lander
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, São Paulo, 13083, Brazil
| | - Miguel A Chiurillo
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, São Paulo, 13083, Brazil
| | - Roberto Docampo
- Departamento de Patologia Clínica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, São Paulo, 13083, Brazil.,Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, 30602, USA
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Bunnik EM, Batugedara G, Saraf A, Prudhomme J, Florens L, Le Roch KG. The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. Genome Biol 2016; 17:147. [PMID: 27381095 PMCID: PMC4933991 DOI: 10.1186/s13059-016-1014-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/20/2016] [Indexed: 02/08/2023] Open
Abstract
Background Gene expression is controlled at multiple levels, including transcription, stability, translation, and degradation. Over the years, it has become apparent that Plasmodium falciparum exerts limited transcriptional control of gene expression, while at least part of Plasmodium’s genome is controlled by post-transcriptional mechanisms. To generate insights into the mechanisms that regulate gene expression at the post-transcriptional level, we undertook complementary computational, comparative genomics, and experimental approaches to identify and characterize mRNA-binding proteins (mRBPs) in P. falciparum. Results Close to 1000 RNA-binding proteins are identified by hidden Markov model searches, of which mRBPs encompass a relatively large proportion of the parasite proteome as compared to other eukaryotes. Several abundant mRNA-binding domains are enriched in apicomplexan parasites, while strong depletion of mRNA-binding domains involved in RNA degradation is observed. Next, we experimentally capture 199 proteins that interact with mRNA during the blood stages, 64 of which with high confidence. These captured mRBPs show a significant overlap with the in silico identified candidate RBPs (p < 0.0001). Among the experimentally validated mRBPs are many known translational regulators active in other stages of the parasite’s life cycle, such as DOZI, CITH, PfCELF2, Musashi, and PfAlba1–4. Finally, we also detect several proteins with an RNA-binding domain abundant in Apicomplexans (RAP domain) that is almost exclusively found in apicomplexan parasites. Conclusions Collectively, our results provide the most complete comparative genomics and experimental analysis of mRBPs in P. falciparum. A better understanding of these regulatory proteins will not only give insight into the intricate parasite life cycle but may also provide targets for novel therapeutic strategies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1014-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelien M Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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Skinner-Adams TS, Sumanadasa SD, Fisher GM, Davis RA, Doolan DL, Andrews KT. Defining the targets of antiparasitic compounds. Drug Discov Today 2016; 21:725-39. [DOI: 10.1016/j.drudis.2016.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/04/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
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Amiri A, Bandani AR, Alizadeh H. MOLECULAR IDENTIFICATION OF CYSTEINE AND TRYPSIN PROTEASE, EFFECT OF DIFFERENT HOSTS ON PROTEASE EXPRESSION, AND RNAI MEDIATED SILENCING OF CYSTEINE PROTEASE GENE IN THE SUNN PEST. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2016; 91:189-209. [PMID: 26609789 DOI: 10.1002/arch.21311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sunn pest, Eurygaster integriceps, is a serious pest of cereals in the wide area of the globe from Near and Middle East to East and South Europe and North Africa. This study described for the first time, identification of E. integriceps trypsin serine protease and cathepsin-L cysteine, transcripts involved in digestion, which might serve as targets for pest control management. A total of 478 and 500 base pair long putative trypsin and cysteine gene sequences were characterized and named Tryp and Cys, respectively. In addition, the tissue-specific relative gene expression levels of these genes as well as gluten hydrolase (Gl) were determined under different host kernels feeding conditions. Result showed that mRNA expression of Cys, Tryp, and Gl was significantly affected after feeding on various host plant species. Transcript levels of these genes were most abundant in the wheat-fed E. integriceps larvae compared to other hosts. The Cys transcript was detected exclusively in the gut, whereas the Gl and Tryp transcripts were detectable in both salivary glands and gut. Also possibility of Sunn pest gene silencing was studied by topical application of cysteine double-stranded RNA (dsRNA). The results indicated that topically applied dsRNA on fifth nymphal stage can penetrate the cuticle of the insect and induce RNA interference. The Cys gene mRNA transcript in the gut was reduced to 83.8% 2 days posttreatment. Also, it was found that dsRNA of Cys gene affected fifth nymphal stage development suggesting the involvement of this protease in the insect growth, development, and molting.
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Affiliation(s)
- Azam Amiri
- Plant Protection Department, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ali Reza Bandani
- Plant Protection Department, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Houshang Alizadeh
- Department of Agronomy & Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Sci Rep 2016; 6:21438. [PMID: 26888608 PMCID: PMC4757839 DOI: 10.1038/srep21438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/18/2016] [Indexed: 02/06/2023] Open
Abstract
Most eukaryotic ribosomes contain 26/28S, 5S, and 5.8S large subunit ribosomal RNAs (LSU rRNAs) in addition to the 18S rRNA of the small subunit (SSU rRNA). However, in kinetoplastids, a group of organisms that include medically important members of the genus Trypanosoma and Leishmania, the 26/28S large subunit ribosomal RNA is uniquely composed of 6 rRNA fragments. In addition, recent studies have shown the presence of expansion segments in the large ribosomal subunit (60S) of Trypanosoma brucei. Given these differences in structure, processing and assembly, T. brucei ribosomes may require biogenesis factors not found in other organisms. Here, we show that one of two putative 3-methylcytidine methyltransferases, TbMTase37 (a homolog of human methyltransferase-like 6, METTL6), is important for ribosome stability in T. brucei. TbMTase37 localizes to the nucleolus and depletion of the protein results in accumulation of ribosomal particles lacking srRNA 4 and reduced levels of polysome associated ribosomes. We also find that TbMTase37 plays a role in cytokinesis, as loss of the protein leads to multi-flagellated and multi-nucleated cells.
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